Dear Brent:
If you know some biology of the TF (or family members) in hand, search
the database for promoters/enhancers for the binding site consensus.
Pick out promoters that look like they might be good (physiologically
relevant) targets based on the expression patterns of the TF and
potential target and whatever other biology is known. Then test them in
cotransfection assays in a relevant cell line. You can also look for
regulation of the endogenous target mRNA by transfection of the TF cDNA,
although that rarely works out. It's always best to start with the
biology, otherwise you might compile a bunch of solid data and then have
the unpleasant task of trying to convince a reviewer why your
neuron-specific TF turns on a liver-specific promoter, for example.
OR, you can do what everybody else is doing.....differential display
using TF+ and TF- cell lines or inducible TF transfectants. Be prepared
for a long term commitment and dealing with the issue of pulling out
physiologically relevant targets.
I'm sure there are other ways, too. These are what first popped into my
head.
Good luck and if you get any other good advice, let me know. I'm a TF
guy, too.
Mark R. Miglarese, Ph.D.
Cancer Research
Pfizer Central Research
Box 372
Eastern Point Road
Groton, CT USA 06340
Phone: (860) 441-8478
FAX: (860) 441-1290
Email: miglaresemr at pfizer.com